SeqGene is an open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, allele specific expression, and expression-genotying association analysis. SeqGene is especially suited for RNA-seq and exonome-seq applications, with focus on protein coding and regulatory regions of a genome. For RNA-seq applications, SeqGene implemented a novel topology-based pathway analysis method to identify SNP-Expression co-enrichment and SNP-Expression paths.
SeqGene supports mutation detection and annotation, dbSNP and 1000 Genome data integration, RNA-Seq expression quantification, mutation and coverage visualization, allele specific expression (ASE), differentially expressed genes (DEGs) identification, copy number variation (CNV) analysis, and gene expression quantitative trait loci (eQTLs) detection. We also developed novel methods for testing the association between SNP and expression and identifying genotype-controlled DEGs.
SeqGene is designed as a general-purpose software package. It supports both paired-end reads and single reads generated on most sequencing platforms; it runs on all major types of computers; it supports arbitrary genome assemblies for arbitrary organisms; and it scales well to support both large and small scale sequencing projects.
The software homepage is http://seqgene.sourceforge.net.
Deng X. (2011) SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. BMC Bioinformatics [Epub ahead of print]. [article]